Suppression of adventitious formation of 8-oxoguanine(TMS)4 from guanine during trimethylsilylation

GC/MS quantitation of 8-oxoguanine derived from DNA may yield artificially high values when trimethylsilylation is used as the technique to form a volatile derivative. Significant quantities of the tetrakis trimethylsilyl-derivative of 8-oxoguanine may be formed from guanine during the derivatization reaction at elevated temperatures. We have screened eight antioxidants in an attempt to identify a substance that will reduce the spurious formation of this product. Whereas several compounds were active, N-phenyl-1-naphthylamine was the most effective agent. Moreover, this compound was sufficiently basic to act as a catalyst for the derivatization reaction. Our data, which are based on the use of an isotopically labeled internal standard, show that the level of the tetrakis trimethylsilyl derivative of 8-oxoguanine remained constant as a function of derivatization heating time when N-phenyl-1-naphthylamine was added to a reaction in which guanine was present. In contrast, the level in control samples increased linearly with reaction time indicating formation of 8-oxoGua during derivatization. The level of 8-oxoguanine was measured in both a synthetic oligodeoxynucleotide containing a single 8-oxo-2'-deoxyguanosine moiety and commercially available calf thymus DNA using this technique.

Mutagenicity and repair of oxidative DNA damage: insights from studies using defined lesions

Oxidative DNA damage has been implicated in mutagenesis, carcinogenesis and aging. Endogenous cellular processes such as aerobic metabolism generate reactive oxygen species (ROS) that interact with DNA to form dozens of DNA lesions. If unrepaired, these lesions can exert a number of deleterious effects including the induction of mutations. In an effort to understand the genetic consequences of cellular oxidative damage, many laboratories have determined the patterns of mutations generated by the interaction of ROS with DNA. Compilation of these mutational spectra has revealed that GC-->AT transitions and GC-->TA transversions are the most commonly observed mutations resulting from oxidative damage to DNA. Since mutational spectra convey only the end result of a complex cascade of events, which includes formation of multiple adducts, repair processing, and polymerase errors, it is difficult if not impossible to assess the mutational specificity of individual DNA lesions directly from these spectra. This problem is especially complicated in the case of oxidative DNA damage owing to the multiplicity of lesions formed by a single damaging agent. The task of assigning specific features of mutational spectra to individual DNA lesions has been made possible with the advent of a technology to analyze the mutational properties of single defined adducts, in vitro and in vivo. At the same time, parallel progress in the discovery and cloning of repair enzymes has advanced understanding of the biochemical mechanisms by which cells excise DNA damage. This combination of tools has brought our understanding of DNA lesions to a new level of sophistication. In this review, we summarize the known properties of individual oxidative lesions in terms of their structure, mutagenicity and repairability.

Different mechanisms of thioredoxin in its reduced and oxidized forms in defense against hydrogen peroxide in Escherichia coli

The present experiments were done to elucidate the roles of thioredoxin and thioredoxin reductase system in defense against hydrogen peroxide (H2O2) in Escherichia coli. The thioredoxin-deficient mutant (trxA) was more sensitive to H2O2 than was the wild-type strain, when challenged in the stationary and exponentially growing phase. Thioredoxin reductase-deficient mutant (trxB) in the stationary phase also exhibited increased sensitivity, compared with the wild-type strain. These results indicated that reduced form of thioredoxin is required for defense against H2O2, possibly by scavenging radicals generated in the cells. In contrast, the trxB mutant in the growing phase had higher survival after exposure to H2O2 than the wild-type strain. The acquirement of resistance related to increased capacity for removing H2O2 in the trxB mutant and was not observed in a catalase-negative background. Furthermore, enhanced expression of the katG :: lacZ gene occurred in the mutant. Therefore, it was concluded that oxidized form of thioredoxin confers H2O2 resistance on E. coli cells by increasing activity to remove H2O2, which was brought about by enhanced induction of the katG-coded catalase/hydroperoxidase I at the transcriptional level. In addition, this resistance to H2O2 correlated well with reduced amount of DNA damage caused by H2O2, determined by the induction level of the recA :: lacZ fusion gene after treatment with H2O2.

Visualizing metal-ion-binding sites in group I introns by iron(II)-mediated Fenton reactions

BACKGROUND

Most catalytic RNAs depend on divalent metal ions for folding and catalysis. A thorough structure-function analysis of catalytic RNA therefore requires the identification of the metal-ion-binding sites. Here, we probed the binding sites using Fenton chemistry, which makes use of the ability of Fe2+ to functionally or structurally replace Mg2+ at ion-binding sites and to generate short-lived and highly reactive hydroxyl radicals that can cleave nucleic acid and protein backbones in spatial proximity of these ion-binding sites.

RESULTS

Incubation of group I intron RNA with Fe2+, sodium ascorbate and hydrogen peroxide yields distinctly cleaved regions that occur only in the correctly folded RNA in the presence of Mg2+ and can be competed by additional Mg2+, suggesting that Fe2+ and Mg2+ interact with the same sites. Cleaved regions in the catalytic core are conserved for three different group I introns, and there is good correlation between metal-ion-binding sites determined using our method and those determined using other techniques. In a model of the T4 phage-derived td intron, cleaved regions separated in the secondary structure come together in three-dimensional space to form several metal-ion-binding pockets.

CONCLUSIONS

In contrast to structural probing with Fe2+/EDTA, cleavage with Fe2+ detects metal-ion-binding sites located primarily in the inside of the RNA. Essentially all metal-ion-binding pockets detected are formed by tertiary structure elements. Using this method, we confirmed proposed metal-ion-binding sites and identified new ones in group I intron RNAs. This approach should allow the localization of metal-ion-binding sites in RNAs of interest.

Analysis of a form of oxidative DNA damage, 8-hydroxy-2'-deoxyguanosine, as a marker of cellular oxidative stress during carcinogenesis

8-hydroxy-2'-deoxyguanosine (8-OH-dG) was first reported in 1984 as a major form of oxidative DNA damage product by heated sugar, Fenton-type reagents and X-irradiation in vitro. 8-OH-dG has been detected in cellular DNA using an HPLC-ECD method in many laboratories. Analyses of 8-OH-dG in animal organ DNA after the administration of oxygen radical-forming chemicals will be useful for assessments of their carcinogenic risk. Its analysis in human leucocyte DNA and in urine is a new approach to the assessment of an individual's cancer risk due to oxidative stress. The increase of the 8-OH-dG level in the cellular DNA, detected by HPLC-ECD method, was supported by its immunochemical detection and its enhanced repair activity. The validity of the general use of 8-OH-dG as a marker of cellular oxidative stress is discussed.

Kinetics of oxidized cytosine repair by endonuclease III of Escherichia coli

Endonuclease III of Escherichia coli excises a broad range of oxidized, hydrated and ring-fragmented pyrimidines from DNA. The kinetic parameters were compared for repair of three potentially mutagenic oxidized cytosine lesions: 5,6-dihydroxy-5, 6-dihydro-2'-deoxyuridine (uracil glycol or Ug), 5-hydroxy-2'-deoxycytidine (5-ohC), and 5-hydroxy-2'-deoxyuridine (5-ohU). Site-specifically modified 40-mer oligonucleotides containing each of the three lesions in the same sequence context were synthesized chemically or by a combination of chemical and enzymatic methods. Appropriately protected phosphoramidites of 5-ohC and 5-ohU were synthesized and incorporated into oligonucleotides by standard solid-phase synthetic methods. The lability of Ug made it necessary to use an alternative approach to prepare the analogous 40-mers containing Ug. An uracil containing pentamer oligonucleotide was oxidized with OsO4 to generate the corresponding Ug containing product, which was then ligated into an oligonucleotide scaffold to generate 40 base pair duplexes. Using 32P-labeled substrates and a gel electrophoresis based assay, the values of Km and Vmax for excision of 5-ohC, 5-ohU, and Ug were determined. In this experimental system, the order of repair efficiency is Ug >> 5-ohC >> 5-ohU based on ratios of Vmax/Km. Modest effects were observed when the base paired opposite the lesion was changed from G to A.

Oxidative damage to DNA constituents by iron-mediated fenton reactions. The deoxycytidine family

Damage by iron-mediated Fenton reactions under aerobic or anaerobic conditions to deoxycytidine, deoxycytidine-5'-monophosphate, d-CpC, d-CpCpC, and dCMP residues in DNA resulted in at least 26 distinguishable products. Of these, 24 were identified by high performance liquid chromatography retention times, radiolabeling, UV absorption spectra, chemical synthesis, fast atom bombardment mass spectrometry, high resolution fast atom bombardment mass spectrometry, and/or NMR. The nature of the products was qualitatively similar for each substrate except for d-CpC (and possibly d-CpCpC) under anaerobic conditions for which 5-hydroxy-deoxycytidine was uniquely present and 1-carbamoyl-1-carboxy-4-(2-deoxy-beta-D-erythropentofuranosyl) glycinamide was uniquely absent. Damage to dC, d-CpC, and d-CpCpC but not to dCMP or DNA was largely quenched by ethanol, indicating that iron is strongly associated only with dCMP and DNA. The presence of oxygen had little effect with dC or dCMP but had quantitative and qualitative effects with d-CpC and a significantly quantitative but not a qualitative effect with DNA. NADH could drive the Fenton reaction to cause damage to the dC family in vitro, consistent with a previous proposal that NADH was the reducing agent for the Fenton reaction in vivo (Imlay, J.A., and Linn, S. (1988) Science 240, 1302-1309). Finally, the damage spectrum of the dC family by the Fenton reaction is compared with that by ionizing radiation and chemical mechanisms leading to the formation of the 24 identified products are proposed.